rs10500505

Variant names:

• chr16-64909123-T-A
• rs10500505
• ENST00000722600.1:n.178-26177A>T

Your query was ambiguous. Multiple possible variants found:

• chr16-64909123-T-A
• chr16-64909123-T-G

Variant summary

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

The ENST00000722600.1(ENSG00000294300):​n.178-26177A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,056 control chromosomes in the GnomAD database, including 3,506 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 0.20 (3506 hom., cov: 32)
• Consequence: ENSG00000294300 ENST00000722600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 4 publications found

Genes affected

ENSG00000294300 (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 (EAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000722600.1. 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
	ENSG00000294300	ENST00000722600.1		n.178-26177A>T		intron	N/A
	ENSG00000294300	ENST00000722601.1		n.73-26177A>T		intron	N/A
	ENSG00000294300	ENST00000722602.1		n.305+1250A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30066 AN: 151938 Hom.: 3503 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30091 AN: 152056 Hom.: 3506 Cov.: 32 AF XY: 0.206 AC XY: 15302 AN XY: 74302

African (AFR) AF: 0.120 AC: 4986 AN: 41512

American (AMR) AF: 0.319 AC: 4866 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2126 AN: 5130

South Asian (SAS) AF: 0.235 AC: 1130 AN: 4816

European-Finnish (FIN) AF: 0.257 AC: 2717 AN: 10574

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13121 AN: 67968

Other (OTH) AF: 0.192 AC: 405 AN: 2112

Alfa AF: 0.0983 Hom.: 157

Bravo AF: 0.200

Asia WGS AF: 0.287 AC: 996 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.77
PhyloP100		-0.65

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: rs10500505;

hg19: chr16-64943026;