6-77452800-A-G

Variant names:

• chr6-77452800-A-G
• rs2143823
• XM_047419660.1:c.-3743+11367A>G

Variant summary

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

The ENST00000741460.1(ENSG00000296734):​n.48+14100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0572 in 152,314 control chromosomes in the GnomAD database, including 471 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 0.057 (471 hom., cov: 33)
• Consequence: ENSG00000296734 ENST00000741460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 4 publications found

Genes affected

LOC105377864 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741460.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296734	ENST00000741460.1		n.48+14100T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0572 AC: 8710 AN: 152196 Hom.: 471 Cov.: 33

Gnomad AFR AF: 0.0875

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0481

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0234

Gnomad OTH AF: 0.0598

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

GnomAD4 genome AF: 0.0572 AC: 8718 AN: 152314 Hom.: 471 Cov.: 33 AF XY: 0.0590 AC XY: 4397 AN XY: 74478

African (AFR) AF: 0.0874 AC: 3631 AN: 41564

American (AMR) AF: 0.0853 AC: 1305 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0481 AC: 167 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1066 AN: 5182

South Asian (SAS) AF: 0.113 AC: 546 AN: 4830

European-Finnish (FIN) AF: 0.0222 AC: 236 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0234 AC: 1590 AN: 68028

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0409 Hom.: 52

Bravo AF: 0.0664

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.2
DANN	Benign	0.32
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2143823; hg19: chr6-78162517;