rs7219464

Variant names:

• chr17-74200252-C-A
• rs7219464
• ENST00000764632.1:n.87-11626G>T

Variant summary

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

The ENST00000764632.1(MGC16275):​n.87-11626G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,810 control chromosomes in the GnomAD database, including 9,911 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 (9911 hom., cov: 30)
• Consequence: MGC16275 ENST00000764632.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 4 publications found

Genes affected

MGC16275 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764632.1. 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
	MGC16275	ENST00000764632.1		n.87-11626G>T		intron	N/A
	MGC16275	ENST00000764633.1		n.47-4799G>T		intron	N/A
	MGC16275	ENST00000764634.1		n.146-11626G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54376 AN: 151692 Hom.: 9892 Cov.: 30

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.359 AC: 54428 AN: 151810 Hom.: 9911 Cov.: 30 AF XY: 0.357 AC XY: 26502 AN XY: 74198

African (AFR) AF: 0.341 AC: 14123 AN: 41376

American (AMR) AF: 0.301 AC: 4587 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1206 AN: 5164

South Asian (SAS) AF: 0.254 AC: 1221 AN: 4800

European-Finnish (FIN) AF: 0.439 AC: 4628 AN: 10536

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.387 AC: 26293 AN: 67900

Other (OTH) AF: 0.333 AC: 700 AN: 2104

Alfa AF: 0.370 Hom.: 9980

Bravo AF: 0.351

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	3.7
DANN	Benign	0.81
PhyloP100		-1.1

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: rs7219464;

hg19: chr17-72196391;