chr10-56773229-C-A

Variant names:

• chr10-56773229-C-A
• rs11005510
• ENST00000777611.1:n.62+31962C>A

Variant summary

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

The ENST00000777611.1(ENSG00000301278):​n.62+31962C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,222 control chromosomes in the GnomAD database, including 210 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 0.037 (210 hom., cov: 33)
• Consequence: ENSG00000301278 ENST00000777611.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154
• Publications: 2 publications found

Genes affected

ENSG00000301278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301278	ENST00000777611.1	n.62+31962C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0371 AC: 5645 AN: 152104 Hom.: 209 Cov.: 33

Gnomad AFR AF: 0.0978

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0247

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00414

Gnomad FIN AF: 0.00264

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0321

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

GnomAD4 genome AF: 0.0371 AC: 5655 AN: 152222 Hom.: 210 Cov.: 33 AF XY: 0.0344 AC XY: 2564 AN XY: 74446

African (AFR) AF: 0.0978 AC: 4061 AN: 41524

American (AMR) AF: 0.0247 AC: 377 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.00414 AC: 20 AN: 4828

European-Finnish (FIN) AF: 0.00264 AC: 28 AN: 10622

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0151 AC: 1027 AN: 68020

Other (OTH) AF: 0.0313 AC: 66 AN: 2112

Alfa AF: 0.0105 Hom.: 8

Bravo AF: 0.0422

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs11005510; hg19: chr10-58532989;