rs1163662

Variant names:

• chr12-80898148-G-A
• rs1163662
• NM_004664.4:c.83-8779C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004664.4(LIN7A):​c.83-8779C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 152,156 control chromosomes in the GnomAD database, including 39,150 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (39150 hom., cov: 33)
• Consequence: LIN7A NM_004664.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.569
• Publications: 1 publications found

Genes affected

LIN7A (HGNC:17787): (lin-7 homolog A, crumbs cell polarity complex component) The protein encoded by this gene is involved in generating and maintaining the asymmetric distribution of channels and receptors at the cell membrane. The encoded protein also is required for the localization of some specific channels and can be part of a protein complex that couples synaptic vesicle exocytosis to cell adhesion in the brain. [provided by RefSeq, May 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004664.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN7A	NM_004664.4	MANE Select	c.83-8779C>T		intron	N/A	NP_004655.1	O14910
	LIN7A	NM_001324423.2		c.-13+39493C>T		intron	N/A	NP_001311352.1
	LIN7A	NR_136887.2		n.67+39493C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LIN7A	ENST00000552864.6	TSL:1 MANE Select	c.83-8779C>T		intron	N/A	ENSP00000447488.1	O14910
	LIN7A	ENST00000549417.5	TSL:1	c.65-8779C>T		intron	N/A	ENSP00000448975.1	H0YIA8
	LIN7A	ENST00000261203.7	TSL:1	n.83-8779C>T		intron	N/A	ENSP00000261203.3	J3KN23

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103395 AN: 152036 Hom.: 39144 Cov.: 33

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.721

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.680 AC: 103418 AN: 152156 Hom.: 39150 Cov.: 33 AF XY: 0.679 AC XY: 50539 AN XY: 74402

African (AFR) AF: 0.338 AC: 14028 AN: 41456

American (AMR) AF: 0.621 AC: 9501 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2678 AN: 3472

East Asian (EAS) AF: 0.610 AC: 3157 AN: 5176

South Asian (SAS) AF: 0.644 AC: 3104 AN: 4822

European-Finnish (FIN) AF: 0.879 AC: 9314 AN: 10596

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.869 AC: 59124 AN: 68016

Other (OTH) AF: 0.719 AC: 1520 AN: 2114

Alfa AF: 0.763 Hom.: 5910

Bravo AF: 0.643

Asia WGS AF: 0.587 AC: 2043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.80
DANN	Benign	0.45
PhyloP100		-0.57
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1163662; hg19: chr12-81291927;