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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903779	XR_007065222.1	n.165+1250A>T		intron_variant	Intron 1 of 1
LOC124903779	XR_007065223.1	n.121+1294A>T		intron_variant	Intron 1 of 1
LOC105371313	XR_933677.2	n.116+574T>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000294300	ENST00000722600.1	n.178-26177A>T		intron_variant	Intron 2 of 2
ENSG00000294300	ENST00000722601.1	n.73-26177A>T		intron_variant	Intron 1 of 1
ENSG00000294300	ENST00000722602.1	n.305+1250A>T		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs10500505; hg19: chr16-64943026;