chr6-74257276-G-T

Variant names:

• chr6-74257276-G-T
• rs763672
• ENST00000435946.1:n.139-89799G>T

Variant summary

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

The ENST00000435946.1(ENSG00000223786):​n.139-89799G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,002 control chromosomes in the GnomAD database, including 10,656 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 0.34 (10656 hom., cov: 32)
• Consequence: ENSG00000223786 ENST00000435946.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 3 publications found

Genes affected

ENSG00000223786 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928516	NR_110856.1	n.139-89799G>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000223786	ENST00000435946.1	n.139-89799G>T		intron_variant	Intron 1 of 3	1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51600 AN: 151884 Hom.: 10658 Cov.: 32

Gnomad AFR AF: 0.0923

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.339 AC: 51603 AN: 152002 Hom.: 10656 Cov.: 32 AF XY: 0.342 AC XY: 25433 AN XY: 74270

African (AFR) AF: 0.0922 AC: 3825 AN: 41502

American (AMR) AF: 0.408 AC: 6235 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1182 AN: 3466

East Asian (EAS) AF: 0.439 AC: 2263 AN: 5160

South Asian (SAS) AF: 0.501 AC: 2411 AN: 4816

European-Finnish (FIN) AF: 0.409 AC: 4304 AN: 10530

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.444 AC: 30187 AN: 67944

Other (OTH) AF: 0.352 AC: 743 AN: 2108

Alfa AF: 0.382 Hom.: 2119

Bravo AF: 0.325

Asia WGS AF: 0.459 AC: 1598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs763672; hg19: chr6-74966992;