rs7770848

Variant names:

• chr6-44801500-T-G
• rs7770848
• ENST00000671451.2:n.196-28088T>G

Variant summary

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

The ENST00000671451.2(ENSG00000286417):​n.196-28088T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0293 in 151,996 control chromosomes in the GnomAD database, including 237 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 0.029 (237 hom., cov: 31)
• Consequence: ENSG00000286417 ENST00000671451.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.114
• Publications: 4 publications found

Genes affected

ENSG00000286417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101929770	XR_007059596.1	n.353-28088T>G		intron_variant	Intron 2 of 2
LOC101929770	XR_007059597.1	n.252-28088T>G		intron_variant	Intron 1 of 1
LOC101929770	XR_007059598.1	n.145-28088T>G		intron_variant	Intron 1 of 1
LOC101929770	XR_926855.3	n.246-28088T>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286417	ENST00000671451.2	n.196-28088T>G		intron_variant	Intron 1 of 2
ENSG00000286417	ENST00000811306.1	n.275-28088T>G		intron_variant	Intron 2 of 3
ENSG00000286417	ENST00000811307.1	n.289-28088T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0293 AC: 4445 AN: 151878 Hom.: 236 Cov.: 31

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0132

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000417

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.000706

Gnomad OTH AF: 0.0192

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

GnomAD4 genome AF: 0.0293 AC: 4455 AN: 151996 Hom.: 237 Cov.: 31 AF XY: 0.0289 AC XY: 2145 AN XY: 74296

African (AFR) AF: 0.100 AC: 4155 AN: 41430

American (AMR) AF: 0.0132 AC: 201 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5176

South Asian (SAS) AF: 0.000418 AC: 2 AN: 4788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.000706 AC: 48 AN: 67972

Other (OTH) AF: 0.0185 AC: 39 AN: 2110

Alfa AF: 0.0156 Hom.: 30

Bravo AF: 0.0324

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.36
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs7770848; hg19: chr6-44769237;