chr6-77456403-A-C

Variant names:

• chr6-77456403-A-C
• rs9359271
• XM_047419660.1:c.-3743+14970A>C

Variant summary

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

The ENST00000741460.1(ENSG00000296734):​n.48+10497T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,992 control chromosomes in the GnomAD database, including 10,639 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 0.36 (10639 hom., cov: 32)
• Consequence: ENSG00000296734 ENST00000741460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 7 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.508 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+10497T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53907 AN: 151874 Hom.: 10621 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.355 AC: 53973 AN: 151992 Hom.: 10639 Cov.: 32 AF XY: 0.356 AC XY: 26483 AN XY: 74298

African (AFR) AF: 0.514 AC: 21292 AN: 41404

American (AMR) AF: 0.348 AC: 5313 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1078 AN: 3472

East Asian (EAS) AF: 0.481 AC: 2476 AN: 5152

South Asian (SAS) AF: 0.478 AC: 2302 AN: 4820

European-Finnish (FIN) AF: 0.237 AC: 2512 AN: 10578

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17856 AN: 67980

Other (OTH) AF: 0.335 AC: 708 AN: 2112

Alfa AF: 0.294 Hom.: 11787

Bravo AF: 0.367

Asia WGS AF: 0.451 AC: 1570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.72
PhyloP100		0.039

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9359271;

hg19: chr6-78166120;